Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF HHARI, A RING-IBR-RING UBIQUITIN LIGASE: AUTOINHIBITION OF AN ARIADNE-FAMILY E3 AND INSIGHTS INTO LIGATION MECHANISM
 
Authors :  D. M. Duda, J. L. Olszewski, B. A. Schulman
Date :  23 Apr 13  (Deposition) - 29 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ring-Ibr-Ring, E3 Ubiquitin Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Duda, J. L. Olszewski, J. P. Schuermann, I. Kurinov, D. J. Miller, A. Nourse, A. F. Alpi, B. A. Schulman
Structure Of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition Of An Ariadne-Family E3 And Insights Into Ligation Mechanism.
Structure V. 21 1030 2013
PubMed-ID: 23707686  |  Reference-DOI: 10.1016/J.STR.2013.04.019

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE ARIH1
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H7-AP2, HHARI, MONOCYTE PROTEIN 6, MOP-6, PROTEIN ARIADNE-1 HOMOLOG, ARI-1, UBCH7-BINDING PROTEIN, UBCM4-INTERACTING PROTEIN, UBIQUITIN-CONJUGATING ENZYME E2-BINDING PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1ZN12Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:344 , CYS A:347 , CYS A:362 , CYS A:367BINDING SITE FOR RESIDUE ZN A 601
02AC2SOFTWARECYS A:372 , CYS A:375 , HIS A:382 , CYS A:389BINDING SITE FOR RESIDUE ZN A 602
03AC3SOFTWARECYS A:276 , CYS A:281 , CYS A:297 , CYS A:299BINDING SITE FOR RESIDUE ZN A 603
04AC4SOFTWARECYS A:304 , CYS A:307 , HIS A:312 , CYS A:317BINDING SITE FOR RESIDUE ZN A 604
05AC5SOFTWARECYS A:186 , CYS A:189 , CYS A:208 , CYS A:211BINDING SITE FOR RESIDUE ZN A 605
06AC6SOFTWARECYS A:203 , HIS A:205 , CYS A:231 , CYS A:236BINDING SITE FOR RESIDUE ZN A 606
07AC7SOFTWARECYS B:344 , CYS B:347 , CYS B:362 , CYS B:367BINDING SITE FOR RESIDUE ZN B 601
08AC8SOFTWARECYS B:372 , CYS B:375 , HIS B:382 , CYS B:389BINDING SITE FOR RESIDUE ZN B 602
09AC9SOFTWARECYS B:276 , CYS B:281 , CYS B:297 , CYS B:299BINDING SITE FOR RESIDUE ZN B 603
10BC1SOFTWARECYS B:304 , CYS B:307 , HIS B:312 , CYS B:317BINDING SITE FOR RESIDUE ZN B 604
11BC2SOFTWARECYS B:186 , CYS B:189 , CYS B:208 , CYS B:211BINDING SITE FOR RESIDUE ZN B 605
12BC3SOFTWARECYS B:203 , HIS B:205 , CYS B:231 , CYS B:236BINDING SITE FOR RESIDUE ZN B 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KBL)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:122 -Val A:123
2Glu A:222 -Glu A:223
3Cys A:299 -Gly A:300
4Gly A:355 -Gly A:356
5Trp A:379 -Glu A:380
6His B:234 -Gly B:235
7Cys B:299 -Gly B:300
8Gly B:355 -Gly B:356

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KBL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KBL)

(-) Exons   (0, 0)

(no "Exon" information available for 4KBL)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhh.........................hhhhhhhhhhhhh....................hhhhhhhhh...hhhhhhhhhhhhhhhhhh..eee........eeee......eee.....eee...........hhhhhhhhhhhh....eee......eee......eee........eee.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbl A  99 YRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLMERYFDGNMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNRSRAALQRYLFYCNRYMNHMQSLRFEHKLYAQVKQKMEWIEVQFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLW 552
                                   108       118       128       138       148    || 188       198       208       218       228       238       248       258       268       278       288       298       308       318       337       347       357       367       377       387     ||409       419       429       439   ||  457       467       477       487       497       507       517       527       537       547     
                                                                                153|                                                                                                                                            327|                                                     393|                                  443|                                                                                                    
                                                                                 184                                                                                                                                             337                                                      406                                   452                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhh.........hhhhh.........hhhhhhhhhhhhhh...................hhhhhh....hhhhhhhhhhhhhhhhhh..eee........eeee......eee.....eee...........hhhhhhhhh........eee......eee......eee........eee........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbl B  99 YRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLMERYFDGPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNERSRAALQRYLFYCNRYMNHMQSLRFEHKLYAQVKQKMEWIEVQFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLWE 553
                                   108       118       128       138       148   ||  190       200       210       220 ||    232       242       252       262       272       282       292       302       312       322     ||340       350       360       370       380       390   ||  411       421       431       441 ||    459       469       479       489       499       509       519       529       539       549    
                                                                               152|                                  222|                                                                                                    328|                                                      394|                                  443|                                                                                                     
                                                                                185                                   225                                                                                                     337                                                       406                                   452
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4KBL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KBL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KBL)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:299 - Gly A:300   [ RasMol ]  
    Cys B:299 - Gly B:300   [ RasMol ]  
    Glu A:122 - Val A:123   [ RasMol ]  
    Glu A:222 - Glu A:223   [ RasMol ]  
    Gly A:355 - Gly A:356   [ RasMol ]  
    Gly B:355 - Gly B:356   [ RasMol ]  
    His B:234 - Gly B:235   [ RasMol ]  
    Trp A:379 - Glu A:380   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4kbl
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARI1_HUMAN | Q9Y4X5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ARI1_HUMAN | Q9Y4X5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARI1_HUMAN | Q9Y4X5: 1wd2 2m9y 4kc9 5udh

(-) Related Entries Specified in the PDB File

4kc9